Bioinformatics approaches for unveiling virus-host interactions

Iuchi, Hitoshi; Kawasaki, Jun; Kubo, Kento; Fukunaga, Tsukasa; Hokao, Koki; Yokoyama, Gentaro; Akiko, Ichinose; Suga, Kanta; Hamada, Michiaki

doi:10.1016/j.csbj.2023.02.044

Cited by 12 publications

(5 citation statements)

References 129 publications

(118 reference statements)

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“…Chronotypes did not exhibit specific taxonomic enrichments, possibly indicating a linear relationship with the diverse number of hosts that follow similar seasonal patterns of abundance. Further analysis, integrating host-derived data (such as amplicon or cellular fraction metagenome-assembled genomes) with viral chronotypes, or an improvement in accuracy of host-prediction from phage genomes [85], may offer better insights into these seasonal relationships and mechanisms of interaction. AMGs play a crucial role in expanding host metabolic capacity and enhancing virus production in marine ecosystems [86,87].…”

Section: Discussionmentioning

confidence: 99%

Viral chronotypes and their role in shaping seasonal viral dynamics in the Western English Channel

Bolaños,

Michelsen,

Temperton

2024

Preprint

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Marine viruses are key players of ocean biogeochemistry, profoundly influencing microbial community ecology and evolution. Despite their importance, few studies have explored the temporal dynamics of viral genome abundances in marine environments. Viral dynamics are complex, influenced by multiple factors such as host population dynamics and environmental conditions. To disentangle the complexity of viral communities, we developed an unsupervised machine learning framework to classify viral genomes into "chronotypes" based on temporal abundance patterns. Analysing an inter-seasonal monthly time-series of surface viral metagenomes from the Western English Channel, we identified chronotypes and compared their functional and evolutionary profiles. Results revealed a consistent annual cycle with steep compositional changes from winter to summer and steadier transitions from summer to winter. Seasonal chronotypes were enriched in potential auxiliary metabolic genes like ferrochelatases and 2OG-Fe(II) oxygenases compared to non-seasonal types. Chronotypes clustered into four groups based on their correlation profiles with environmental parameters, primarily driven by temperature and nutrients. Viral genomes exhibited a rapid turnover of polymorphisms, akin to Red Queen dynamics. However, within seasonal chronotypes, some sequences exhibited annual polymorphism recurrence, which declined over a 16-month period, suggesting that a fraction of the seasonal viral populations evolve more slowly. Classification into chronotypes revealed viral genomic signatures linked to temporal patterns, likely reflecting metabolic adaptations to environmental fluctuations and host dynamics. This novel framework enables the identification of long-term trends in viral composition, environmental influences on genomic structure, and potential viral interactions.

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Section: Discussionmentioning

confidence: 99%

Viral chronotypes and their role in shaping seasonal viral dynamics in the Western English Channel

Bolaños,

Michelsen,

Temperton

2024

Preprint

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“…With the longest genome among RNA viruses, members of this viral family express up to 29 proteins, engaging in intricate interactions with the host proteome. Understanding these interactions is crucial for identifying the cellular pathways exploited by these viruses to replicate and evade innate immunity [ 47 , 48 , 49 , 50 ]. A recent study focused on the relationship between host–virus PPIs, particularly on the involvement of disordered protein regions binding to folded protein domains in the virus life cycle.…”

Section: Fundamentals Of Viral Protein Interactionsmentioning

confidence: 99%

Exploring Viral–Host Protein Interactions as Antiviral Therapies: A Computational Perspective

Idrees,

Chen,

Panth

et al. 2024

Microorganisms

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The interactions between human and viral proteins are pivotal in viral infection and host immune responses. These interactions traverse different stages of the viral life cycle, encompassing initial entry into host cells, replication, and the eventual deployment of immune evasion strategies. As viruses exploit host cellular machinery for their replication and survival, targeting key protein–protein interactions offer a strategic approach for developing antiviral drugs. This review discusses how viruses interact with host proteins to develop viral–host interactions. In addition, we also highlight valuable resources that aid in identifying new interactions, incorporating high-throughput methods, and computational approaches, ultimately helping to understand how these tools can be effectively utilized to study viral–host interactions.

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“…The use of bioinformatics tools to analyze the growing data from fields like molecular biology, genomics, transcriptomics, and proteomics is getting has achieved significant success [146]. In combination with bioinformatics, the utilization of NGS technology has evolved into a formidable instrument for characterizing and scrutinizing human pathogens.…”

Section: Bioinformatics Toolsmentioning

confidence: 99%

Genomics for Emerging Pathogen Identification and Monitoring: Prospects and Obstacles

Vashisht,

Mondal

et al. 2023

BioMedInformatics

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Emerging infectious diseases (EIDs) pose an increasingly significant global burden, driven by urbanization, population explosion, global travel, changes in human behavior, and inadequate public health systems. The recent SARS-CoV-2 pandemic highlights the urgent need for innovative and robust technologies to effectively monitor newly emerging pathogens. Rapid identification, epidemiological surveillance, and transmission mitigation are crucial challenges for ensuring public health safety. Genomics has emerged as a pivotal tool in public health during pandemics, enabling the diagnosis, management, and prediction of infections, as well as the analysis and identification of cross-species interactions and the categorization of infectious agents. Recent advancements in high-throughput DNA sequencing tools have facilitated rapid and precise identification and characterization of emerging pathogens. This review article provides insights into the latest advances in various genomic techniques for pathogen detection and tracking and their applications in global outbreak surveillance. We assess methods that leverage pathogen sequences and explore the role of genomic analysis in understanding the epidemiology of newly emerged infectious diseases. Additionally, we address technical challenges and limitations, ethical and legal considerations, and highlight opportunities for integrating genomics with other surveillance approaches. By delving into the prospects and obstacles of genomics, we can gain valuable insights into its role in mitigating the threats posed by emerging pathogens and improving global preparedness in the face of future outbreaks.

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Bioinformatics approaches for unveiling virus-host interactions

Cited by 12 publications

References 129 publications

Viral chronotypes and their role in shaping seasonal viral dynamics in the Western English Channel

Viral chronotypes and their role in shaping seasonal viral dynamics in the Western English Channel

Exploring Viral–Host Protein Interactions as Antiviral Therapies: A Computational Perspective

Genomics for Emerging Pathogen Identification and Monitoring: Prospects and Obstacles

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